Contacts of the helix formed by residues 678 - 688 (chain F) in PDB entry 4OQB
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASP 678 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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674F LYS 3.5 20.4 + - - +
675F MET* 4.1 7.2 + - - +
676F ILE 3.7 1.2 - - - -
677F PHE* 1.3 74.0 - - - +
679F VAL* 1.3 64.3 + - - +
680F GLU* 3.4 17.4 + - - +
681F SER* 3.2 38.5 + - - +
682F MET* 3.6 12.6 + - - +
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Residues in contact with VAL 679 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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677F PHE* 3.2 17.4 + - + +
678F ASP* 1.3 70.6 + - - +
680F GLU* 1.3 60.2 + - - +
681F SER 3.2 2.0 - - - -
682F MET* 3.1 17.2 + - + +
683F LYS* 2.8 27.9 + - + +
771F ILE* 4.1 14.6 - - + +
774F ALA* 5.3 7.9 - - + +
775F TYR* 3.3 47.1 - - + +
778F LEU* 4.1 21.3 - - + -
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Residues in contact with GLU 680 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
678F ASP* 3.4 10.9 + - - +
679F VAL* 1.3 76.7 - - - +
681F SER* 1.3 62.1 + - - +
683F LYS* 3.4 20.4 + - + +
684F LYS* 3.2 21.8 + - - +
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Residues in contact with SER 681 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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675F MET 5.7 2.2 - - - -
678F ASP* 3.2 34.7 + - - +
679F VAL 3.2 0.4 - - - -
680F GLU* 1.3 78.2 - - - +
682F MET* 1.3 61.3 + - - +
684F LYS* 3.7 9.7 + - - +
685F ALA* 3.2 20.3 + - - +
866F THR* 6.2 3.6 - - - -
867F THR* 5.0 2.0 - - - +
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Residues in contact with MET 682 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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675F MET 5.5 0.7 - - - +
676F ILE* 3.1 31.9 - - - +
677F PHE* 4.6 3.4 - - - -
678F ASP 3.6 11.0 - - - +
679F VAL* 3.1 24.1 + - + +
681F SER* 1.3 76.5 - - - +
683F LYS* 1.3 64.4 + - - +
685F ALA* 3.3 13.7 + - - +
686F MET* 3.4 2.4 + - - +
771F ILE* 3.4 41.1 - - + +
774F ALA* 4.0 25.8 - - + -
866F THR 4.7 0.9 - - - +
867F THR* 3.6 49.4 - - + +
870F ALA* 4.2 0.7 - - + -
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Residues in contact with LYS 683 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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679F VAL* 2.8 17.0 + - + +
680F GLU* 3.5 22.7 - - + +
681F SER 3.3 0.4 - - - -
682F MET* 1.3 73.6 - - - +
684F LYS* 1.3 65.5 + - - +
686F MET* 2.9 19.8 + - - +
687F VAL* 3.3 13.7 + - - +
693F LEU* 4.2 9.5 - - + +
697F PRO* 3.9 26.1 - - + +
771F ILE* 5.2 2.9 - - + -
775F TYR* 3.2 26.2 + - + +
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Residues in contact with LYS 684 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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680F GLU 3.2 10.6 + - - +
681F SER* 3.7 12.0 + - - +
682F MET 3.4 0.2 - - - -
683F LYS* 1.3 77.9 - - - +
685F ALA* 1.3 64.1 + - - +
687F VAL* 3.0 29.6 + - + +
688F GLU* 4.0 7.1 + - - +
911F SER* 5.9 0.4 + - - -
914F ASP* 4.9 16.8 - - - +
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Residues in contact with ALA 685 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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681F SER 3.2 12.4 + - - +
682F MET* 3.3 15.0 - - - +
683F LYS 3.1 0.8 - - - -
684F LYS* 1.3 80.5 - - - +
686F MET* 1.3 61.9 + - + +
688F GLU* 3.3 31.6 - - - +
689F TYR* 3.6 2.8 - - - -
865F ARG* 3.5 25.4 + - - +
867F THR* 4.1 13.2 - - + -
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Residues in contact with MET 686 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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682F MET 3.6 3.1 - - - +
683F LYS* 2.9 11.8 + - - +
685F ALA* 1.3 80.1 - - + +
687F VAL* 1.3 64.0 + - - +
688F GLU 3.2 2.5 - - - -
689F TYR* 3.1 39.9 + - + +
690F GLU 3.4 8.0 + - - -
691F ILE* 3.7 24.7 + - + +
693F LEU* 4.4 7.0 - - + -
764F MET* 4.5 2.2 - - - +
767F ASN* 3.5 26.5 - - + -
768F LEU* 4.0 28.5 - - + -
771F ILE* 3.4 33.0 - - + -
865F ARG* 4.0 5.2 - - - +
867F THR* 5.8 1.3 - - - +
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Residues in contact with VAL 687 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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683F LYS 3.3 12.3 + - - +
684F LYS* 3.0 23.2 + - + +
686F MET* 1.3 76.6 - - - +
688F GLU* 1.3 62.3 - - - +
690F GLU* 3.2 16.8 + - - +
691F ILE 5.3 0.9 - - - -
693F LEU* 3.5 37.2 - - + -
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Residues in contact with GLU 688 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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684F LYS* 4.0 6.6 + - - +
685F ALA* 3.3 28.4 - - - +
687F VAL* 1.3 79.5 - - - +
689F TYR* 1.3 70.9 + - + +
690F GLU* 3.4 8.8 + - - +
865F ARG* 3.0 24.5 + - - -
909F HIS* 5.9 0.3 - - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il